Right guard Dominick Puni left the game during the starters' lone drive and did not return.
"Dominick Puni left with a knee, never returned," Shanahan told reporters. "It'll be a few weeks—possible PCL."
The coach isn't dismissing the possibility that Puni could suit up for the first game of the regular season. Obviously, we've seen the last of the second-year offensive lineman during the preseason.
Two running backs also exited the game. Patrick Taylor suffered a dislocated shoulder and is expected to miss a "couple of weeks," while Corey Kiner sustained a high-ankle sprain and will miss multiple weeks.
The injuries add to a growing list of setbacks the 49ers have dealt with throughout training camp, putting pressure on the team's depth.
"You just deal with it," Shanahan said. "Hopefully, we'll get a bunch of guys back here. I mean, we didn't lose anyone for the year or anything like that. And we had pretty good luck on defense and special teams today, so that was good."
Shanahan added: "Losing those three guys on offense was tough, but they won't be out forever, so hopefully, they'll heal up fast."
The 49ers now turn their attention to their final preseason matchup, a home game against the Los Angeles Chargers at Levi's Stadium. After that, Shanahan and his team will prepare for their Week 1 divisional showdown against the Seattle Seahawks at Lumen Field.
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